|
| Status |
Public on Oct 06, 2021 |
| Title |
S3_control LSD rep3 |
| Sample type |
SRA |
| |
|
| Source name |
control LSD_whole larvae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: wild type
developmental stage: 3rd instar larvae
treatment: LSD (low sugar diet, 10% yeast)
tissue: whole larvae
|
| Growth protocol |
1st instar larvae were collected 24 hours after egg laying to plates with LSD (low sugar diet, 10% yeast) at a controlled density. Early 2nd instar larvae were transferred at 48 hours after egg laying to plates containing either LSD or HSD (high sugar diet, 10% yeast supplemented with 15% sugar). After 8 hours of diet exposure, 20 larvae per sample were collected and snap-frozen in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The larvae were homogenised and total RNA was extracted with the Nucleospin RNA II kit (Macherey-Nagel) according to the manufacturer’s instruction.
Libraries were prepared with the TruSeq Stranded mRNA kit (Illumina), and RNA-sequencing was performed to an average depth of 20 million reads per sample with Illumina NextSeq500 technology using the 75bp cycle kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
A003_3_ACAGTG_run20191126N_S3
|
| Data processing |
Sequenced reads were trimmed with Trimmomatic with parameters ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36
Sequences were mapped using TopHat (v2.1.0) to dmel R6.10 with parameter -p 4 and quantified with HTSeq (v2.7.6) with parameters -m HTSeq.scripts.count -m union -s reverse -a 10 -t exon -i Parent
Differentially expressed genes were calculated with R package limma with Benjamini-Hochberg correction, with genes with low counts (cpm<1 in more than one replicate) filtered
Genome_build: Flybase Drosophila melanogaster R6.10
Supplementary_files_format_and_content: grn_all_comparisons.txt file includes read counts for expressed genes for all samples and their statistics
|
| |
|
| Submission date |
Feb 12, 2021 |
| Last update date |
Oct 06, 2021 |
| Contact name |
Krista Kokki |
| Organization name |
University of Helsinki
|
| Department |
Department of Biosciences (Genetics)
|
| Lab |
Hietakangas lab
|
| Street address |
Viikinkaari 9, Biocenter 1, Institute of Biotechnology P.O.Box. 56
|
| City |
Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE166681 |
Metabolic gene regulation by Drosophila GATA transcription factor Grain |
|
| Relations |
| BioSample |
SAMN17889822 |
| SRA |
SRX10086244 |
